Brainiac confronts Kara at the Kent farm and demands that she go with him. After she refuses, he promises Clark and her that due to her defiance someone will be hurt. Realizing that Clark will need all the advantages he can to face Brainiac, Kara decides to teach him how to fly. Meanwhile, Lois and Jimmy team up to do a story on Patricia Swann’s murder.
Lex recalls a moment from his childhood that had been repressed since the first meteor shower. He had wandered off while playing with Patricia Swann, Jason Teague, and Oliver Queen during one of their father’s Veritas group meetings. Lex overheard the three men discussing their plan to put an envelope that contained something very powerful that pertained to the “alien traveler” their group had sworn to protect in a lockbox in Zurich. Back in the present, Lex believes that the key in the locket he had Patricia Swann’s killer retrieve from her dead body will open that lockbox. He gives his personal assistant 24 hours to find out where exactly this lockbox is in Zurich.
Lois and Jimmy suspect that Lionel was behind Patricia Swann’s murder since he was the last person she talked to before she was killed. They corner Lionel at LuthorCorp, but he denies having had anything to do with the murder. Meanwhile, Brainiac confronts Lana at the Isis Foundation and uses his built-in technology to take full control of her central nervous system. This process makes her fully aware of her surroundings, but helpless to do anything other than what Brainiac allows.
Since Clark can’t get over his fear of heights, making it impossible for Kara to teach him how to fly, he has to take another approach to going after Brainiac. Knowing that Brainiac feeds on energy, he has Chloe scan the world’s power grids for any unusual surges of energy. They discover that the most recent unusual surge occurred at the Isis Foundation. When Clark arrives at the building, he finds the place empty except for Lionel. While Lionel doesn’t know Lana’s whereabouts, he begs Clark to listen to him, intending to tell him about a second key that he has for the lockbox in Zurich. Wanting nothing to do with Lionel, Clark storms out of the building to look for Lana. He’s horrified when he finds her at the farm in a catatonic state. She scribbles down a message from Brainiac that asks Kara to meet him on top of the Daily Planet building. Suspecting that Brainiac had originally intended to do what he did to Lana to her, Kara takes full blame and decides to go by herself to the Daily Planet and confront him.
After discovering that Lionel had been to the Isis Foundation earlier that day, Lois and Jimmy sneak into the empty building and find an envelope that Lionel left for Lana. The envelope contains pictorial proof that Lex hired Patricia’s limo driver to murder her. Meanwhile, Lex’s personal assistant informs him that she has found out where the lockbox is in Zurich but that opening it requires two different keys. After remembering another repressed memory from his childhood, Lex realizes that his father has the second key.
Clark finds Kara with Brainiac on top of the Daily Planet building. Brainiac explains what he has done to Lana and states that only he has the technology to undo it. Suspecting that Brainiac will return Lana to normal if she gives herself up to him, Kara bids farewell to Clark and leaves with her nemesis. The two fly high up into the air and vanish, leaving Clark with no clue as to their whereabouts or his cousin’s fate. Meanwhile, Lionel begs Chloe to talk to Clark for him. He insists that becoming Jor’El’s emissary changed his life by making him strive to be better person, and that protecting Clark is his way of repenting for past misdeeds. Chloe doesn’t believe he is telling the truth, nor does she believe he is serious when he says Clark is in great danger due to something terrible that will soon occur.
In the end, Clark takes Lana to an institution where she can be looked after until he can find a way to bring her out of the catatonic state Brainiac put her in. As he bids her farewell, she murmurs that it is too late. Unsure of what awaits the love of his life, Clark breaks down after putting his hands over her eyes and gently closing them for her.
Starring: Tom Welling (Clark Kent), Michael Rosenbaum (Lex Luthor), Kristin Kreuk (Lana Lang), Allison Mack (Chloe Sullivan), Erica Durance (Lois Lane), Aaron Ashmore (Jimmy Olsen), Laura Vandervoort (Kara), John Glover (Lionel Luthor)
Guest Starring: James Marsters (Brainiac), Jonathan Scarfe (Robert Queen), Rick Ravanello (Edward Teague), Connor Stanhope (Young Lex Luthor), Luke Gair (Young Oliver Queen), Owen Best (Young Jason Teague), Conner Dwelly (Young Patricia Swann), Anna Galvin (Gina), Mike Donis (Orderly), David Lovgren ()
Written by Brain Peterson & Kelly Souders
Directed by James Marshall